The Conformation of the ε- and γ-Subunits within the Escherichia coli F₁ ATPase

F₁ is the water-soluble portion of the ubiquitous F ₁F₀ ATP synthase. Its structure includes three α- and three β-subunits, arranged as a hexameric disc, plus a γ-subunit that penetrates the center of the disc akin to an axle. Recently Hausrath et al. (Hausrath, A. C., Grüber, G., Matthews, B. W., and Capaldi, R. A. (1999) Proc. Natl. Acad. Sci. U. S. A. 96, 13697-13702) obtained an electron density map of E. coli F₁ at 4.4-Å resolution in which the coiled-coil α-helices of the γ-subunit could be seen to extend 45 Å from the base of the α₃β₃ hexamer. Subsequently the structure of a truncated form of the E. coli γ-subunit in complex with ε has been described (Rodgers, A. J. W., and Wilce, M. C. J. (2000) Nat. Struct. Biol. 7, 1051-1054). In the present study the 4.4-Å resolution electron density map of E. coli F₁ is re-evaluated in light of the newly available data on the γ- and ε-subunits. It is shown that the map of the F₁ complex is consistent with the structure of the isolated subunits. When E. coli F₁ is compared with that from beef heart, the structures of the E. coli γ- and ε-subunits are seen to be generally similar to their counterparts in the bovine enzyme but to undergo major shifts in position. In particular, the two long, coiled-coil α-helices that lie along the axis of F₁ both unwind and rotate. Also the ε-subunit rotates around the axis by 81° and undergoes a net translation of about 23 Å. It is argued that these large-scale changes in conformation reflect distinct functional states that occur during the rotation of the γ-subunit within the α₃β₃ hexamer.